This user guide provides practical guidance for operating the Environmental eXternalities ACcounting Tool (EX-ACT) online app for assessing environmental externalities in agrifood system interventions. It focuses on helping users navigate the interface, understand the structure of the tool, and apply its functions to estimate greenhouse gas emissions, carbon stock changes, and other environmental outcomes. This manual ensures consistent application of the tool and complements but does not replace the methodological information provided in the EX-ACT handbook.The user guide reflects the version of the EX-ACT online application available as of December 2025 and is intended for a broad range of users, including project managers, analysts, policymakers and technical partners. It supports ex ante, mid-term and ex post assessments, highlighting the tool’s capacity to incorporate country-specific data, connect with external datasets and GIS platforms, and enhance the consistency and transparency of environmental accounting across land-based, livestock-based and value chain interventions. The guide is structured in two parts. Part 1 introduces the overall architecture, navigation and core functionalities of the online application. Part 2 provides detailed guidance on the use of modules and specific features for assessing environmental externalities within the EX-ACT online application. Through clear and practical instructions, the guide facilitates accurate, efficient and user-friendly application of EX-ACT to support climate-resilient and environmentally sustainable decision-making.